Datasets
The README links benchmark and dataset catalogues rather than fixing one data release.
Open Problems is an extensible platform hosting benchmark tasks and their datasets.
The README links benchmark and dataset catalogues rather than fixing one data release.
No platform-wide scientific metric applies: hosted task definitions select their own evaluator.
inapplicable
Inputs are specified by each hosted task.
Conceptual procedure. Task variants and protocol versions retain their separate scoring conditions.
limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
accuracy (fraction) · Higher values are better.
Open Problems label projection CENGEN-BATCH-ACCURACY: Label projection on CeNGEN (split by batch), Accuracy · CeNGEN (split by batch) (Open Problems label projection split)
Evidence origin: Author-reported evaluation.
openproblems-label primary benchmark evidence · results, dataset(cengen_batch), metric(accuracy)Every method Open Problems label projection reports on Label projection on CeNGEN (split by batch), Accuracy, scored with Accuracy on CeNGEN (split by batch).
Automated source review: 2026-09-18. Numerical source review does not establish independent reproduction.
Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.
Showing 12 of 16 matching rows.
Open Problems is a collection of separately versioned single-cell evaluation tasks. Each task defines its inputs, reference data, methods, controls and metrics. For example, label projection learns from reference labels and predicts a held-out dataset, whereas integration measures how supplied batches are combined.
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
These source-backed links do not make different protocols or scores interchangeable.
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
No concrete protocols are explicitly linked to this suite. Protocol identification and baseline selection are outstanding.
Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-09-29-06401fd5b220. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Open Problems links task-specific repositories and contribution documentation. The inspected label-projection repository specifies AnnData inputs, prediction outputs and evaluation components, but these READMEs do not supply a complete end-to-end shell run. Select a released task workflow, executor and resource bundle before running; the platform itself has no universal single command.
A maintained rewire runner has not been verified for this benchmark. Check data access, weights, licences, dependencies and hardware in the linked official documentation; requirements have not been fully extracted.
openproblems-bio/openproblems / README.md; openproblems-bio/task_label_projection / README.md · Platform README.md lines 9–18; task_label_projection/README.md Description and API sectionsPrimary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction.
Stable record: discovery-benchmark-open-problemsExplanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | The README links benchmark and dataset catalogues rather than fixing one data release.Sourcesopenproblems-bio/openproblems official source · Pinned README: platform description and benchmark/dataset resource links |
| Splits | No platform-wide split exists: select a hosted benchmark task and its dataset protocol. · Not applicableSourcesopenproblems-bio/openproblems official source · Pinned README: platform description and benchmark/dataset resource links |
| Metrics | No platform-wide scientific metric applies: hosted task definitions select their own evaluator. · Not applicableSourcesopenproblems-bio/openproblems official source · Pinned README: platform description and benchmark/dataset resource links |
| Baselines | No single platform-wide baseline: methods and references belong to each hosted task. · Not applicableSourcesopenproblems-bio/openproblems official source · Pinned README: platform description and benchmark/dataset resource links |
| Leakage controls | Controls are task dependent. Label Projection v1.0.0 distinguishes training/test batches and includes both random and batch-based CeNGEN dataset variants. Other tasks, such as batch integration, evaluate transductive processing of the supplied cells; a universal held-out-cell rule would be misleading.Sourcesopenproblems-label primary benchmark evidence · Label Projection v1.0.0: task description, dataset variants and controls |
| Uncertainty | The inspected task pages and reporting configuration do not prescribe one platform-wide bootstrap or repeated-seed interval. Individual task versions define datasets, metrics and runs; model uncertainty from a method such as scANVI is not benchmark-score uncertainty. · Not reported in inspected sourcesSourcesopenproblems-label primary benchmark evidence · Label Projection v1.0.0: task description, dataset variants and controls |
| Entity type | Platform hosting computational biology benchmark tasks.Sourcesopenproblems-bio/openproblems official source · Pinned README: platform description and benchmark/dataset resource links |
| Organisms | Organisms belong to the selected task and dataset; the platform defines no unique organism. · Not applicableSourcesopenproblems-bio/openproblems official source · Pinned README: platform description and benchmark/dataset resource links |
| Assays | The platform does not prescribe one assay. · Not applicableSourcesopenproblems-bio/openproblems official source · Pinned README: platform description and benchmark/dataset resource links |
| Allowed inputs | Inputs are specified by each hosted task.Sourcesopenproblems-bio/openproblems official source · Pinned README: platform description and benchmark/dataset resource links |
| Adaptation | Adaptation rules belong to the task implementation; the platform is not a fitted predictor. · Not applicableSourcesopenproblems-bio/openproblems official source · Pinned README: platform description and benchmark/dataset resource links |
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Last literature check: 2026-09-17. Primary-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.
| Paper or primary resource | Version | Reference |
|---|---|---|
| Defining and benchmarking open problems in single-cell analysis | PMC full-text XML snapshot PMC11030530 at retrieval; byte-pinned by SHA-256 | Read source DOI: 10.21203/rs.3.rs-4181617/v1 |
| openproblems-label primary benchmark evidence | v1.0.0 | Read source |
The catalogue now holds 384 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.
primary protocol screened
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
19 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual procedure. Task variants and protocol versions retain their separate scoring conditions. Individual claims | openproblems-bio/openproblems official source Pinned README: platform description and benchmark/dataset resource links Version: 0ca5d0cd040b741c1b6cc2e4cad7230cb2c50131 | source checked automated source review · 2026-09-16 Audit detailsPrimary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Diagram steps
| openproblems-bio/openproblems official source Pinned README: platform description and benchmark/dataset resource links Version: 0ca5d0cd040b741c1b6cc2e4cad7230cb2c50131 | source checked automated source review · 2026-09-16 Audit detailsPrimary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Evaluation procedure Individual claims | openproblems-bio/openproblems official source Pinned README: platform description and benchmark/dataset resource links Version: 0ca5d0cd040b741c1b6cc2e4cad7230cb2c50131 | source checked automated source review · 2026-09-16 Audit detailsPrimary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets The README links benchmark and dataset catalogues rather than fixing one data release. Individual claims | openproblems-bio/openproblems official source Pinned README: platform description and benchmark/dataset resource links Version: 0ca5d0cd040b741c1b6cc2e4cad7230cb2c50131 | source checked automated source review · 2026-09-16 Audit detailsPrimary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits No platform-wide split exists: select a hosted benchmark task and its dataset protocol. Individual claims | openproblems-bio/openproblems official source Pinned README: platform description and benchmark/dataset resource links Version: 0ca5d0cd040b741c1b6cc2e4cad7230cb2c50131 | inapplicable automated source review · 2026-09-16 Audit detailsPrimary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Adaptation rules belong to the task implementation; the platform is not a fitted predictor. Individual claims | openproblems-bio/openproblems official source Pinned README: platform description and benchmark/dataset resource links Version: 0ca5d0cd040b741c1b6cc2e4cad7230cb2c50131 | inapplicable automated source review · 2026-09-16 Audit detailsPrimary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics No platform-wide scientific metric applies: hosted task definitions select their own evaluator. Individual claims | openproblems-bio/openproblems official source Pinned README: platform description and benchmark/dataset resource links Version: 0ca5d0cd040b741c1b6cc2e4cad7230cb2c50131 | inapplicable automated source review · 2026-09-16 Audit detailsPrimary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines No single platform-wide baseline: methods and references belong to each hosted task. Individual claims | openproblems-bio/openproblems official source Pinned README: platform description and benchmark/dataset resource links Version: 0ca5d0cd040b741c1b6cc2e4cad7230cb2c50131 | inapplicable automated source review · 2026-09-16 Audit detailsPrimary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls Controls are task dependent. Label Projection v1.0.0 distinguishes training/test batches and includes both random and batch-based CeNGEN dataset variants. Other tasks, such as batch integration, evaluate transductive processing of the supplied cells; a universal held-out-cell rule would be misleading. Individual claims | openproblems-label primary benchmark evidence Label Projection v1.0.0: task description, dataset variants and controls Version: v1.0.0 | source checked automated source review · 2026-09-16 Audit detailsPrimary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Uncertainty The inspected task pages and reporting configuration do not prescribe one platform-wide bootstrap or repeated-seed interval. Individual task versions define datasets, metrics and runs; model uncertainty from a method such as scANVI is not benchmark-score uncertainty. Individual claims | openproblems-label primary benchmark evidence Label Projection v1.0.0: task description, dataset variants and controls Version: v1.0.0 | unreported automated source review · 2026-09-16 Audit detailsPrimary paper and/or task implementation reviewed for the explicitly cited methodology claims. Scope-limited absence is recorded only after the documented source search; no model runs or independent reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
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Release 2026-09-29-06401fd5b220 · Record review: discovered
Stable ID: discovery-benchmark-open-problems